Mothur bioinformatics pipeline

Summary report

Metadata profiling

Original OTU table

# A tibble: 6 × 16
  label Group  numOtus Otu01 Otu02 Otu03 Otu04 Otu05 Otu06 Otu07 Otu08 Otu09
  <dbl> <chr>    <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1  0.03 F3D0        13     1     0     0     0     0     0     0     0     0
2  0.03 F3D1        13     0     1     0     0     0     0     0     0     0
3  0.03 F3D141      13     1     1     0     0     0     0     0     0     0
4  0.03 F3D144      13     1     0     0     1     0     0     0     0     0
5  0.03 F3D147      13     1     0     1     0     0     0     0     0     0
6  0.03 F3D148      13     0     0     1     0     0     1     0     0     1
# … with 4 more variables: Otu10 <dbl>, Otu11 <dbl>, Otu12 <dbl>, Otu13 <dbl>

Tidy OTU long table

# A tibble: 6 × 3
  sample_id otu   count
  <chr>     <chr> <dbl>
1 F3D0      otu01     1
2 F3D1      otu02     1
3 F3D141    otu01     1
4 F3D141    otu02     1
5 F3D141    otu10     1
6 F3D144    otu01     1

Tidy OTU wide table

# A tibble: 6 × 11
  otu    F3D0  F3D1 F3D141 F3D144 F3D147 F3D148  F3D2  F3D6  F3D8  M1D1
  <chr> <dbl> <dbl>  <dbl>  <dbl>  <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl>
1 otu01     1     0      1      1      1      0     0     0     0     0
2 otu02     0     1      1      0      0      0     0     0     0     1
3 otu10     0     0      1      0      0      0     0     0     0     0
4 otu04     0     0      0      1      0      0     0     0     0     2
5 otu03     0     0      0      0      1      1     0     0     0     1
6 otu06     0     0      0      0      0      1     0     0     0     1
[1] "Dimension of the phylotype table table is 13 rows and 11 columns"

Original taxonomy table

# A tibble: 6 × 3
  OTU    Size Taxonomy                                                          
  <chr> <dbl> <chr>                                                             
1 Otu01     4 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(1…
2 Otu02     3 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(1…
3 Otu03     3 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(1…
4 Otu04     3 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(1…
5 Otu05     2 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(1…
6 Otu06     2 Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(1…

Tidy taxonomy table

# A tibble: 6 × 8
  otu   pretty_otu kingdom  phylum        class       order         family genus
  <chr> <chr>      <chr>    <chr>         <chr>       <chr>         <chr>  <chr>
1 otu01 OTU 1      Bacteria Bacteroidetes Bacteroidia Bacteroidales Porph… Barn…
2 otu02 OTU 2      Bacteria Bacteroidetes Bacteroidia Bacteroidales Porph… Porp…
3 otu03 OTU 3      Bacteria Bacteroidetes Bacteroidia Bacteroidales Porph… Porp…
4 otu04 OTU 4      Bacteria Bacteroidetes Bacteroidia Bacteroidales Porph… Porp…
5 otu05 OTU 5      Bacteria Bacteroidetes Bacteroidia Bacteroidales Porph… Porp…
6 otu06 OTU 6      Bacteria Bacteroidetes Bacteroidia Bacteroidales Porph… Porp…